I wonder whether it's because they are putting too much pressure on Warner and Wade to make big scores. Half the interviews I read with Clarke or the Aussie staff talk about how the top order should be getting hundreds. I'm not sure that should be the aim. Eventually, yes. But only if you get past 20 and probably towards 40-50 should you be thinking, 'yeah I'll set myself for a 100 here'.
There's also that awful cliche of 'play your natural game' (the answer to every batsman's problems...
), but in ODIs Warner doesn't seem to know what that natural game is, perhaps Wade too. Even when Warner does make a 100, it's been awkward eg. that 100 vs SL in the 2nd final last summer, came off 140 balls and Clarke outscored him badly during their partnership. His 'natural game' radar is especially screwed if the opposition use spinners to him, because even though he'd like to hit out to break the shackles, it seems he also wants to play responsibly. After that, it's just a matter of which voice/instinct speaks louder.
What's the answer? Could try him down the order so he can hit more gaps in the field early in his innings. Could give him a break from ODIs and try and get him more experience in domestic OD matches. Could just drop him outright. Could give him a better, more experienced opening partner eg. Hussey or Watson, which might make him feel less responsibility and make him play a bit more freely (although the Watson/Warner partnership failed hard in WI and England...). I'm not sure what the ultimate solution is, but I think Warner is most likely the key to fixing these issues with the top order - something needs to happen.